You should do like what Bob J said about the bracket upgrades. These sound pretty good, however I don't have them due to upgrading before I learned about them.
You can also try the soundwedge boxes and put good speakers in them. These I have and they are a good upgrade over stock performance.
If you really want bass that doesn't take up alot of bass try the Infinity Basslink powered sub. It's demensions are 14 1/2'"Wx13 3/8"Hx9 7/8"D, or you could try a Kenwood wOOx powered sub. Both are at Crutchfeild.com